What is the difference between combining 2 actions in one box, and using 2 actions together for one effect?

When using 2 separate actions for 1 effect, you add together all stones of effect from both actions.  This allows you to use more stones than either AN would normally allow.

For example if our hero, Generic Heroman (Acrobatics 3, Close Combat 3), was on top of a roof and wanted to jump down(3 stones into Acrobatics) and land on the bad guy, smacking him in the face with his elbow (3 stones into Close Combat), he could combine the two for 6 stones of effect.

If you combine the 2 actions into one box, that same action would look like this:

Our hero, Generic Heroman (Combat Acrobatics 3), was on top of a roof and wanted to jump down and land on the bad guy, smacking him in the face with his elbow (3 stones into Combat Acrobatics). His total attack would be 3 stones.

It should be noted, that while the second example's attack was weaker, it was only one action, allowing him one more for the panel.